In the last few years, Molecular Dynamics (MD) simulations, coupling with Markov State models (MSMs) have been widely applied to understand the mechanism of complex process in biomolecules and predict long timescale dynamics from a pool of short simulations which solves the timescale issue in conventional MD simulations. However, the limitation of the MSMs is that the accuracy of results significantly relies on the rare events being reversibly sampled in the whole MD simulations. In this work, we built MSMs constructed from the simulations data predicting the folding pathway and folding rate of a designed -helical hairpin, Z34C which are in good agreement with experimental results, while unfolding rate is underestimated. Here we proposed a protocol for enhancing the sampling and improving the accuracy by 1.) obtaining a dominant pathway from a MSMs, 2.) speeding up the transition in that pathway using umbrella sampling method and 3.) estimating the thermodynamics and kinetics information from a multiensemble Markov model (MEMM).<br/>

Markov state model with multiensemble Markov model improving the accuracy in non-equilibrium molecular dynamics simulations

Macromolecular Chemistry: The Second Century

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ACS Spring 2020 National Meeting & Expo

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.